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Found 1 Document (0.526 seconds)

BMRB: 11064

2MUS

Solid-state NMR assignment of the rigid core of the HET-s(218-289) prion protein in its amyloid conformation.

Authors

Siemer, A., Wasmer, C., Lange, A., Van Melckebeke, H., Ernst, M., Ritter, C.H., Steinmetz, M.O., Riek, R., Meier, B.H.

Assembly

HET-s(218-289)

Entity

1. HET-s(218-289) (polymer, Thiol state: not present), 79 monomers, 8650.510 Da Detail

MKIDAIVGRN SAKDIRTEER ARVQLGNVVT AAALHGGIRI SDQTTNSVET VVGKGESRVL IGNEYGGKGF WDNHHHHHH

Formula weight

8650.51 Da

Source organism

Podospora anserina

Exptl. method

solid-state NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 77.2 %, Completeness: 74.5 %, Completeness (bb): 75.8 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	74.5 % (315 of 423)	74.1 % (249 of 336)	75.9 % (66 of 87)
Backbone	75.8 % (232 of 306)	75.8 % (172 of 227)	75.9 % (60 of 79)
Sidechain	71.0 % (132 of 186)	70.8 % (126 of 178)	75.0 % (6 of 8)
Aromatic	51.7 % (15 of 29)	50.0 % (14 of 28)	100.0 % (1 of 1)
Methyl	84.4 % (38 of 45)	84.4 % (38 of 45)

1. HET-s(218-289)

MKIDAIVGRN SAKDIRTEER ARVQLGNVVT AAALHGGIRI SDQTTNSVET VVGKGESRVL IGNEYGGKGF WDNHHHHHH

Show sample condition

Sample #1

Pressure 1 atm, Temperature 278 (±2) K, pH 7.5, Details "Wet" fibrils sample: the total amount of water in the sample is at least 60% (weight). Below, the concentration is given with respect to the total protein concentration.

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

Sample #2

#	Name	Isotope labeling	Type	Concentration
3	HET-s(218-289)	[2-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
4	H2O	natural abundance		7.5 ~ 0.0 mg

Sample #3

#	Name	Isotope labeling	Type	Concentration
5	HET-s(218-289)	[U-10% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
6	H2O	natural abundance		7.5 ~ 0.0 mg

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantan	methine carbon	31.47 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.41 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantan	methine carbon	31.47 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.41 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantan	methine carbon	31.47 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: 0.68 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 4 models in PDB: 2MUS, Strand ID: A, B, C, D, E Detail

Release date

2009-06-24

Citation 1

A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation
Lange, A., Gattin, Z., Van Melckebeke, H., Wasmer, C., Soragni, A., Van Gunsteren, W.F., Meier, B.H.
Chembiochem. (2009), 10, 1657-1665, PubMed 19504509 , DOI 10.1002/cbic.200900019 , Abstract

Show more 2 citaions

Citation 2

Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core
Wasmer, C., Lange, A., Van Melckebeke, H., Siemer, A., Riek, R., Meier, B.H.
Science (2008), 319, 1523-1526, PubMed 18339938 , DOI 10.1126/science.1151839 , Abstract

Citation 3

13C, 15N resonance assignment of parts of the HET-s prion protein in its amyloid form
Siemer, A., Ritter, C., Steinmetz, M.O., Ernst, M., Riek, R., Meier, B.H.
J. Biomol. NMR (2006), 34, 75-87, PubMed 16518695 , DOI 10.1007/s10858-005-5582-7 , Abstract

Hide non-primary 2 citaions

Related entities 1. HET-s(218-289), : 1 : 3 : 1 : 2 entities Detail

Interaction partners 1. HET-s(218-289), : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 DREAM

Instrument

Bruker Avance - 600 MHz

Sample

State solid, Pressure 1 atm, Temperature 278 (±2) K, pH 7.5, Details "Wet" fibrils sample: the total amount of water in the sample is at least 60% (weight). Below, the concentration is given with respect to the total protein concentration.

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

2 TOBSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

3 PDSD No1

Instrument

Bruker Avance - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

4 NCA

Instrument

Bruker Avance - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

5 NCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

6 N(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

7 N(CO)CB

Instrument

Bruker Avance - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

8 N(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

9 CA-CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 mg

10 PDSD No2

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	HET-s(218-289)	[2-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
4	H2O	natural abundance		7.5 ~ 0.0 mg

11 PDSD No3

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	HET-s(218-289)	[U-10% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
6	H2O	natural abundance		7.5 ~ 0.0 mg

12 DQSQ

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
5	HET-s(218-289)	[U-10% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
6	H2O	natural abundance		7.5 ~ 0.0 mg

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_11064_2mus.nef
Input source #2: Coordindates	2mus.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
F	1	3LS	3''',4'-bis(carboxymethyl)-2,2':5',2'':5'',2''':5''',2''''-quinquethiophene-5,5''''-dicarboxylic acid	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---220-----230-------240-------250-------260-------270-------280-------290-----
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
--------10--------20--------30--------40--------50--------60--------70---------

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

---220-----230-------240-------250-------260-------270-------280-------290-----
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
--------10--------20--------30--------40--------50--------60--------70---------

Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C

---220-----230-------240-------250-------260-------270-------280-------290-----
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
--------10--------20--------30--------40--------50--------60--------70---------

Entity_assembly_ID (NMR): D vs Auth_asym_ID (model): D

---220-----230-------240-------250-------260-------270-------280-------290-----
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
--------10--------20--------30--------40--------50--------60--------70---------

Entity_assembly_ID (NMR): E vs Auth_asym_ID (model): E

---220-----230-------240-------250-------260-------270-------280-------290-----
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVKTVVGKGESRVLIGNEYGGKGFWDNHHHHHH
--------10--------20--------30--------40--------50--------60--------70---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	79	100.0
B	B	79	100.0
C	C	79	100.0
D	D	79	100.0
E	E	79	100.0

Content subtype: combined_11064_2mus.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	326		72.2 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 72.2%
- Total number of assignments
  - ¹³C chemical shifts: 260
  - ¹⁵N chemical shifts: 66
- Completeness of assignments
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Keywords amyloid fibril, asparagine ladders, beta-helix, beta-solenoid, HET-s(218-289), hydrophobic core, parallel beta-sheets, prion, salt bridges

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Found 1 Document (0.526 seconds)

BMRB: 11064

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HET-s(218-289), : 1 : 3 : 1 : 2 entities Detail

Interaction partners 1. HET-s(218-289), : 1 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 2 contents Detail